Stem formation simulation

When Nakato et al. incorporated adsorption and desorption of halides into their mathematical description, the new type of oscillations could be reproduced in simulations [57], Furthermore, the calculations revealed that oscillations D required, besides the poisoning of the electrode by halide adsorption, the transient current due to the upd-H formation. Hence, the oscillations necessitate two N-NDR hiding factors the adsorption of a poison and an additional current (stemming from a transient process and not a independent current carrier as in Strasser s type HN-NDR subcategory 3). This led the authors to introduce a new HN-NDR subcategory 4. 

Apparently, the core of the procedure is the mutation operation, because this routine folds new structures, derived from those previously formed. Also, it is clear that this is the part of the algorithm, which allows to implement kinetic effects into the simulation. As mentioned above, disruption and formation of stems may be considered as elementary reactions in multistep RNA folding. Similar to the Monte Carlo procedure, at any given step of simulation a choice between different possible reactions can be made using their probabilities that depend on rate constants. Therefore addition and removal of stems with non-uniform probability distributions can mimic dynamic RNA folding, and different approximations may increase the efficiency of the algorithm. We consider separately some of these approximations, because they represent essential features of RNA dynamics. 

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